Daniel P. Flaherty

Assistant Professor of Medicinal Chemisry and Molecular Pharmacology
Specialization: Medicinal Chemistry and Chemical Biology, Fragment-based drug design


B.A. - 2005 - Central College, Pella, IA
Ph.D. - 2010 - University of Nebraska Medical Center (Mentor: Jonathan Vennerstrom)
Postdoc - 2010 - 2014 - University of Kansas, Specialized Chemistry Center (Mentor: Jeffrey Aube)



Society is losing the battle against drug-resistant bacteria.  The current pace of antibiotic development is woefully behind the rapid emergence of drug-resistant pathogens.  There has been a call by numerous agencies for renewed investment into antibiotic research in order to combat the growing threat of drug-resistance in the so-called ESKAPE pathogens.  Further compounding the problem is that antibiotic research over the last 50 years has centered on chemical modifications to existing antimicrobial chemotypes, for which there are already resistance mechanisms, rather than develop new antibiotics with unique mechanisms of action.  Thus, there is an urgent need to: 1) validate novel antimicrobial targets; 2) explore new antimicrobial chemical space; and 3) develop fresh approaches for targeting previously validated antimicrobial therapeutic targets. To this end, research in my lab utilizes chemical biology and medicinal chemistry principles to validate novel antimicrobial therapeutic targets and design new strategies to inhibit existing antimicrobial targets resulting in an expansion of antimicrobial chemical space.  

Inhibitors of E. coli RNase E: RNA degradation is an essential cellular process that until recently has never been exploited for antibiotic development.  Gram-positive bacteria employ an array of ribonucleases to degrade mRNA and essentiality of each ribonuclease varies by species.  Gram-negative pathogens, on the other hand, use a highly conserved endoribonuclease known as RNase E to carry out this function. Furthermore, RNase E also mediates a second essential process needed for translation, tRNA/rRNA maturation,which could result in dual inhibition of two key cellular processes.  This, coupled with the fact that there is no RNase E ortholog in humans, makes RNase E an attractive candidate for broad spectrum Gram-negative antibiotic development.  My lab uses a two-pronged traditional screening and fragment-based screening approach to identify first-in-class inhibitors for this target.  These molecules will be utilized for target validation and begin to expand novel antimicrobial chemical space into new frontiers.


Drug repositioning to explore novel antimicrobial chemical space:  Work by my lab and our collaborators has identified the antihistamine, terfenadine, to have previously unreported antimicrobial activity.  Therefore, we set out to study the structure-activity relationship of this compound as it pertains to antimicrobial activity.  We have been able to synthesize and test 84 analogs to improve activity versus a panel of Gram-positive pathogens and M. tuberculosis from 16 μg/mL to 1 μg/mL.  We have also shown that these compounds are active against membrane compromised and efflux pump deficient strains of Gram-negative species.  Through microarray and bioassay data we have been able to show that terfenadine and it's analogs are novel bacterial topoisomerase inhibitors, an area of active research in the pharmaceutical industry.  The project will continue to focus on improving potency versus Gram-positive species and MTb while modulating physicochemical properties to reduce known hERG liabilities. 

Methods utilized in my laboratory:  My lab handles projects from the hit identification stage to analog optimization.  We utilize protein thermal shift to screen libraries for binders to targets we are interested in.  For fragment based approaches we take advantage of superb facilities here at Purdue to validate hits via a variety of methods including isothermal titration calorimetry, surface-plasmon resonance, bio-layer interferometry and X-ray crystallography.  For non-fragment hits we work with collaborators to collect enzymatic and whole-cell data on the compounds of interest.  Finally, when applicable, my laboratory pursues inhibitors using structure-based design.  A main priority of my lab is to focus on structure-property relationships as much as structure-activity relationships for our compounds. Members of my laboratory not only design and synthesize all compounds but also participate in collection of biological data.  This provides the students and post-docs with a well-rounded experience to know how both the compounds and biological data are generated.

Service and Engagement

Member of the American Chemical Society, Organic and Medicinal Chemistry Divisions.


MCMP 204 - Organic Chemistry I

Representative Publications

1. Perlmutter, J. I.; Forbes, L. T.; Krysan, D. J.; Ebsworth-Mojica, E.; Dunman, P. M.; Flaherty, D. P.; Repurposing the antihistamine terfenadine for antimicrobial activity against Staphylococcus aureus. J. Med. Chem. 2014, 57, 8540 - 8562

2. Flaherty, D. P.; Miller, J. R.; Garshott, D. M.; Hedrock, M.; Gosalia, P.; Li, Y.; Milewski, M.; Sugarman, E.; Suyama, E.; Nguyen, K.; Vasile, S.; Salaniwal, S.; Stonich, D.; Su, Y.; Vicchiarelli, M.; Chung, T. D. Y.; Pinkerton, A. B.; Aubé, J.; Callaghan, M. U.; Golden, J. E.' Fribley, A. M.; Kaufman, R. J. Discovery and development of selective activators targeting the apoptotic CHOP pathway of the unfolded protein response. ACS Med. Chem. Lett. 2014, 5, 1278 - 1283.

3. Matharu, D. S.; Flaherty, D. P.; Simpson, D. S; Chung, D.; Yan, D.; Noah, J. W.; Jonsson, C. B.; White, E. L.; Aubé, J.; Plemper, R. K.; Severson, W. E.; Golden, J. E.  Optimization of potent and selective quinazolinediones: inhibitors of respiratory syncytial virus that block RNA-dependent-RNA-polymerase complex activity. J. Med. Chem. 2014, 57, 10314 – 10328.

4. Flaherty, D. P.; Simpson, D. S.; Miller, M.; Maki, B. E.; Zou, B.; Shi, J.; Wu, M.; McManus, O. B.; Aubé, J.; Li, M.; Golden, J. E. Potent and selective inhibitors of the TASK-1 potassium channel through chemical optimization of a bis-amide scaffold. Bioorg. Med. Chem. Lett. 2014, 24, 8540 - 8562.

5. Harris, M. T.; Walker, D. M.; Drew, M. E.; Mitchell, W. G.; Dao, K.; Schroeder, C. E.; Flaherty, D. P.; Weiner, W. S.; Golden, J. E.; Morris, J. C. Interrogating a hexokinase-selected small molecule library for inhibitors of Plasmodium falciparum hexokinase. Antimicrob. Agents Chemother. 2013, 57, 3731 - 3737.

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